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Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City

Omicron is the most mutated SARS-CoV-2 variant—a factor that can affect transmissibility, disease severity, and immune evasiveness. Its genomic surveillance is important in cities with millions of inhabitants and an economic center, such as Mexico City. Results. From 16 November to 31 December 2021,...

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Autores principales: Cedro-Tanda, Alberto, Gómez-Romero, Laura, de Anda-Jauregui, Guillermo, Garnica-López, Dora, Alfaro-Mora, Yair, Sánchez-Xochipa, Sonia, García-García, Eulices F., Mendoza-Vargas, Alfredo, Frías-Jiménez, Emmanuel J., Moreno, Bernardo, Campos-Romero, Abraham, Moreno-Camacho, José L., Alcantar-Fernández, Jonathan, Ortíz-Ramírez, Jesús, Benitez-González, Mariana, Trejo-González, Roxana, Aguirre-Chavarría, Daniel, Núñez-Martínez, Marcela E., Uribe-Figueroa, Laura, Angulo, Ofelia, Ruiz, Rosaura, Hidalgo-Miranda, Alfredo, Herrera, Luis A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8950183/
https://www.ncbi.nlm.nih.gov/pubmed/35336952
http://dx.doi.org/10.3390/v14030545
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author Cedro-Tanda, Alberto
Gómez-Romero, Laura
de Anda-Jauregui, Guillermo
Garnica-López, Dora
Alfaro-Mora, Yair
Sánchez-Xochipa, Sonia
García-García, Eulices F.
Mendoza-Vargas, Alfredo
Frías-Jiménez, Emmanuel J.
Moreno, Bernardo
Campos-Romero, Abraham
Moreno-Camacho, José L.
Alcantar-Fernández, Jonathan
Ortíz-Ramírez, Jesús
Benitez-González, Mariana
Trejo-González, Roxana
Aguirre-Chavarría, Daniel
Núñez-Martínez, Marcela E.
Uribe-Figueroa, Laura
Angulo, Ofelia
Ruiz, Rosaura
Hidalgo-Miranda, Alfredo
Herrera, Luis A.
author_facet Cedro-Tanda, Alberto
Gómez-Romero, Laura
de Anda-Jauregui, Guillermo
Garnica-López, Dora
Alfaro-Mora, Yair
Sánchez-Xochipa, Sonia
García-García, Eulices F.
Mendoza-Vargas, Alfredo
Frías-Jiménez, Emmanuel J.
Moreno, Bernardo
Campos-Romero, Abraham
Moreno-Camacho, José L.
Alcantar-Fernández, Jonathan
Ortíz-Ramírez, Jesús
Benitez-González, Mariana
Trejo-González, Roxana
Aguirre-Chavarría, Daniel
Núñez-Martínez, Marcela E.
Uribe-Figueroa, Laura
Angulo, Ofelia
Ruiz, Rosaura
Hidalgo-Miranda, Alfredo
Herrera, Luis A.
author_sort Cedro-Tanda, Alberto
collection PubMed
description Omicron is the most mutated SARS-CoV-2 variant—a factor that can affect transmissibility, disease severity, and immune evasiveness. Its genomic surveillance is important in cities with millions of inhabitants and an economic center, such as Mexico City. Results. From 16 November to 31 December 2021, we observed an increase of 88% in Omicron prevalence in Mexico City. We explored the R346K substitution, prevalent in 42% of Omicron variants, known to be associated with immune escape by monoclonal antibodies. In a phylogenetic analysis, we found several independent exchanges between Mexico and the world, and there was an event followed by local transmission that gave rise to most of the Omicron diversity in Mexico City. A haplotype analysis revealed that there was no association between haplotype and vaccination status. Among the 66% of patients who have been vaccinated, no reported comorbidities were associated with Omicron; the presence of odynophagia and the absence of dysgeusia were significant predictor symptoms for Omicron, and the RT-qPCR Ct values were lower for Omicron. Conclusions. Genomic surveillance is key to detecting the emergence and spread of SARS-CoV-2 variants in a timely manner, even weeks before the onset of an infection wave, and can inform public health decisions and detect the spread of any mutation that may affect therapeutic efficacy.
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spelling pubmed-89501832022-03-26 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City Cedro-Tanda, Alberto Gómez-Romero, Laura de Anda-Jauregui, Guillermo Garnica-López, Dora Alfaro-Mora, Yair Sánchez-Xochipa, Sonia García-García, Eulices F. Mendoza-Vargas, Alfredo Frías-Jiménez, Emmanuel J. Moreno, Bernardo Campos-Romero, Abraham Moreno-Camacho, José L. Alcantar-Fernández, Jonathan Ortíz-Ramírez, Jesús Benitez-González, Mariana Trejo-González, Roxana Aguirre-Chavarría, Daniel Núñez-Martínez, Marcela E. Uribe-Figueroa, Laura Angulo, Ofelia Ruiz, Rosaura Hidalgo-Miranda, Alfredo Herrera, Luis A. Viruses Article Omicron is the most mutated SARS-CoV-2 variant—a factor that can affect transmissibility, disease severity, and immune evasiveness. Its genomic surveillance is important in cities with millions of inhabitants and an economic center, such as Mexico City. Results. From 16 November to 31 December 2021, we observed an increase of 88% in Omicron prevalence in Mexico City. We explored the R346K substitution, prevalent in 42% of Omicron variants, known to be associated with immune escape by monoclonal antibodies. In a phylogenetic analysis, we found several independent exchanges between Mexico and the world, and there was an event followed by local transmission that gave rise to most of the Omicron diversity in Mexico City. A haplotype analysis revealed that there was no association between haplotype and vaccination status. Among the 66% of patients who have been vaccinated, no reported comorbidities were associated with Omicron; the presence of odynophagia and the absence of dysgeusia were significant predictor symptoms for Omicron, and the RT-qPCR Ct values were lower for Omicron. Conclusions. Genomic surveillance is key to detecting the emergence and spread of SARS-CoV-2 variants in a timely manner, even weeks before the onset of an infection wave, and can inform public health decisions and detect the spread of any mutation that may affect therapeutic efficacy. MDPI 2022-03-06 /pmc/articles/PMC8950183/ /pubmed/35336952 http://dx.doi.org/10.3390/v14030545 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Cedro-Tanda, Alberto
Gómez-Romero, Laura
de Anda-Jauregui, Guillermo
Garnica-López, Dora
Alfaro-Mora, Yair
Sánchez-Xochipa, Sonia
García-García, Eulices F.
Mendoza-Vargas, Alfredo
Frías-Jiménez, Emmanuel J.
Moreno, Bernardo
Campos-Romero, Abraham
Moreno-Camacho, José L.
Alcantar-Fernández, Jonathan
Ortíz-Ramírez, Jesús
Benitez-González, Mariana
Trejo-González, Roxana
Aguirre-Chavarría, Daniel
Núñez-Martínez, Marcela E.
Uribe-Figueroa, Laura
Angulo, Ofelia
Ruiz, Rosaura
Hidalgo-Miranda, Alfredo
Herrera, Luis A.
Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City
title Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City
title_full Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City
title_fullStr Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City
title_full_unstemmed Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City
title_short Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City
title_sort early genomic, epidemiological, and clinical description of the sars-cov-2 omicron variant in mexico city
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8950183/
https://www.ncbi.nlm.nih.gov/pubmed/35336952
http://dx.doi.org/10.3390/v14030545
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